SLC2A9 p.Ser461=
c.1383C>T · rs772321208 · VCV1917079
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.03%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.6 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 9.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.03%
Admixed American · 18/60,008 alleles
Filtering AF
0.0194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.016%
Overall
0.00173%
28/1,614,040 alleles · ultra-rare
exomes 22/1,461,838 · genomes 6/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.03% | 3,334 |
| African / African-American | 0.00267% | 37,465 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000508% | 196,673 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SLC2A9
- Protein
- p.Ser461=
- Coding
- c.1383C>T
- MANE Select
- NM_020041
- dbSNP
- rs772321208
- Type
- single nucleotide variant
- Location
- chr4:9834917 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.79 · 7 PDB
- Residue 461
- an α-helix
Similar variants
- SLC2A9 c.681+1G>T Likely pathogenic ★★ same type
- SLC2A9 p.Leu75Arg Pathogenic/Likely pathogenic ★★ same type
- SLC2A9 p.Thr125Met Likely pathogenic ★★ ⚠ same type
- SLC2A9 p.Arg380Gln Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Arg447Trp Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Asn144Ser Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Ile149Val Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Ile207Val Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/slc2a9-p-ser461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown